Well, the cheapest option is to open the door panel and look at the speaker. See if the wires are loose, or look bad. If you have a volt meter, see if you can check for continuity from the head unit to the speaker. It should be 0 ohms
If it's anything more than 0 (a couple tenths or hundreths of an Ohm are okay), then the wire is either grounding out or is corroded, which would be an even bigger problem. After almost almost 2 decades of replacing car stereos on my own cars, I have never actually had a wire go bad.
If the speaker obviously looks bad (torn "surround," the foam around the cone) or makes a grating noise if you push on the cone (don't try with tweeters), then it should be replaced. Sometimes, even the cheap stuff from Best Buy is better than stock. If you have any other speakers you know work (like... from the other side of the car), try swapping 'em out. If the crackling follows the speaker, you know it's bad. If it follows the location, then it's either wiring or the head unit.
If replacing the speaker doesn't help and the wiring is ok, the next option is to get a new head unit. In this case, the cheap crap from Best Buy again is probably better than stock, but that's no reason to get some knock-off brand from Wal-mart. If you recognize the name, it's probably good. Sony, Kenwood, JVC, Pioneer (my fav, for some reason), Alpine, Rockford Fosgate, all decent brands. Best Buy also does installs, and if you don't know jack about car audio, I suggest letting them do it.
Aside from that, if the crackling noise persists, even with a new stereo, I would suggest going to the doctor. A bad sinus infection could be placing pressure on your ear canal, and movement of your head would cause a simulated crackling noise. I doubt that's the problem though...